It sounds like you have a solid understanding of how to do it... before you make it all pretty and tucked in nice and neat, perhaps connect mostly everything (in priority order... subwoofer after amp, amp after head unit, etc.) and make sure it all runs right.. that way its less moving and more rewiring until the wires are perfect... then the trick becomes tucking them away without messing them up.
I think that as long as your head unit supports an equalizer, you shouldn't lose any functionality there.
Don't forget about your in-line fuse coming off of (and remaining near) your battery for the power cable on your amp, lest your car spontaneously "Flame On".
If its of any merit, I believe the power cables can interfere with the signals in the speaker cables if they are too close, but I have not experienced this firsthand. I only have vague hearsay and a hypothesis.
I have shared what I know about regarding your topics. May the force be with you, and may that woman find abundant calories.
I'm not as skilled with the car dismantling, but the concept of the wiring, I get.